When the competitions started, there were no seeding done. All the names are drawn from the pots to match the clubs. Then some clubs protested that some stronger clubs play each other in earlier rounds and at the same time if a weak club gets another weak club, then at least a weak club goes to the next round while a strong club is eliminated.
UEFA has used several systems to prevent such abnormalities.
At first they seeded the clubs who placed in the last eight in the competitions, but this created uneven pictures in the competitions. Sometimes there were not enough seeds and sometimes there were more than enough seeds and the seeds have to play each others.
Then they started to make up club rankings, the same way country rankings were done.
But this way a club from a stronger country may not be seeded if they havenít competed in the last five years. So UEFA decided to mix the Country rankings into Club Rankings. The clubs are seeded according to their country rankings if their club ranking is less. The latest change combine these two rankings. The half of the country rankings are added to each clubís club ranking.(Note: While making the club rankings the same system Country rankings were made is used. The only exception to the system is that the results of all Qualification rounds are erased and not included.)

UEFA CHAMPIONS LEAGUE

Qualification Rounds 1,2,3:
When the number of clubs playing for a round is determined, then half of these numbers are seeded for the round according to UEFA Club rankings.
QR1 and QR2 draws are made at the same time, and QR3 draw is made before QR2 is played. It could happened that a club playing an earlier round ccan also be seeded for the following rounds even though they havenít qualified to that round yet. In those cases the pairing of earlier rounds are seeded and if the seed loses that early round, then the unseeded club takes over the seedís position in the next round.League Stage 1: (32 clubs)
The clubs are placed in four pots. Basically a club is drawn from each pot for groups.
But during the draw some exceptions may be done. A group can not have more than one club from the same country. For TV audience shares some clubs from a country are paired so that they are not placed in the same day schedule.League Stage 2: (16 clubs)
The clubs placed into four pots. The first two pot includes the clubs winning their groups in LS1 and the other two for the LS1 second clubs.
Again the draw is done by drawing a club from each pot.
Same exceptions are applied again.Quarter Finals: (8 clubs)
The group winners of LS2 are seeded and they play the second leg at home.Semi Finals:
No seeding is done.

UEFA CUP

The seeding is rather straight forward in this cup. When the participating clubs are known half of the are seeded. However UEFA makes some grouping before the draw with half of the clubs in each group are seeds. They call these groups geographical grouping, but somehow there are no geographical relations in most cases.
Some geograhical grouping results from this year:
ValŤncia CF (ESP) plays a Russian team, Parma (ITA) plays a team from Finland, Chelsea (ENG) plays a Bulgarian team, Fiorentina (ITA) plays an Ukranian team, Ajax (NED) plays a team from Cyprus, AEK (GRE) plays a Scottish team, GenÁlerbirliūi (TUR) plays a Swedish team, etc.
We canít understand the logic behind this "geograhy".
They make these geographical grouping until Round 3.
No seeding is done starting from the Quarter Finals.

UEFA INTERTOTO CUP

The seeding is different in this cup, since the club rankings are not used. The seeding is done using the country rankings alone.

Round 1: (40 clubs)
Only 16 of the 20 pairings have a seed and 4 pairings donít.Round 2: (32 clubs)
Only 12 of the 16 pairings have a seed and 4 pairings donít. Seeds start from this round.Round 3: (24 clubs)
Only 8 of the 12 pairings have a seed and 4 pairings donít. Seeds start from this round.
No seeding is done after Round 3.